{
  "_id": "6a55c371ff0138dec5d6899a",
  "Package": "occugene",
  "Version": "1.73.0",
  "Date": "2006-11-07",
  "Title": "Functions for Multinomial Occupancy Distribution",
  "Author": "Oliver Will <oliverrreader@gmail.com>",
  "Maintainer": "Oliver Will <oliverrreader@gmail.com>",
  "Description": "Statistical tools for building random mutagenesis\nlibraries for prokaryotes. The package has functions for\nhandling the occupancy distribution for a multinomial and for\nestimating the number of essential genes in random transposon\nmutagenesis libraries.",
  "License": "GPL (>= 2)",
  "biocViews": "Annotation, Pathways",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:32:04 UTC",
  "RemoteUrl": "https://github.com/bioc/occugene",
  "RemoteRef": "HEAD",
  "RemoteSha": "07cdca33f01c249a8819e08fb643141dc24b7c86",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-14 05:00:53 UTC",
    "User": "root"
  },
  "_user": "bioc",
  "_type": "src",
  "_file": "occugene_1.73.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/ce28daed35f680243a26e5f0e889e78be51086b578b6d46d65bea89bdbe13ecb",
  "_filesize": 218716,
  "_sha256": "ce28daed35f680243a26e5f0e889e78be51086b578b6d46d65bea89bdbe13ecb",
  "_expires": "2026-10-22T05:04:47.000Z",
  "_created": "2026-07-14T05:00:53.000Z",
  "_published": "2026-07-14T05:04:49.204Z",
  "_bioccheck": {
    "error": 1,
    "warning": 6,
    "note": 12
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29307292903",
  "_status": "success",
  "_upstream": "https://github.com/bioc/occugene",
  "_commit": {
    "id": "07cdca33f01c249a8819e08fb643141dc24b7c86",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777379524
  },
  "_maintainer": {
    "name": "Oliver Will",
    "email": "oliverrreader@gmail.com"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 87003543935,
      "time": 142,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8300766348"
    },
    {
      "job": 87003543959,
      "time": 163,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8300771980"
    },
    {
      "job": 87003543953,
      "time": 199,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8300781058"
    },
    {
      "job": 87003543899,
      "time": 64,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8300745075"
    },
    {
      "job": 87003543960,
      "time": 79,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8300748699"
    },
    {
      "job": 87003228926,
      "time": 137,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8300727577"
    },
    {
      "job": 87003543937,
      "time": 81,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8300749546"
    },
    {
      "job": 87003543925,
      "time": 65,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8300746031"
    },
    {
      "job": 87003543947,
      "time": 63,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8300744741"
    },
    {
      "job": 87003543929,
      "time": 61,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8300744301"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.0.0",
      "role": "Depends"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.73.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.72.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "annotation",
    "pathways"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 446,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 410,
    "source": "https://www.bioconductor.org/packages/stats/bioc/occugene"
  },
  "_searchresults": 2,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/occugene.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "checkFormat",
    "delta0",
    "eMult",
    "etDelta",
    "fCumul",
    "fFit",
    "occup2Negenes",
    "unbiasB0",
    "unbiasDelta0",
    "varMult"
  ],
  "_datasets": [
    {
      "name": "sampleAnnotation",
      "title": "Annotation for a Hypothetical Prokayote",
      "object": "sampleAnnotation",
      "file": "sampleAnnotation.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "idNum",
        "first",
        "last",
        "orientation"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    },
    {
      "name": "sampleInsertions",
      "title": "Insertions for a Hypothetical Clonal Library",
      "object": "sampleInsertions",
      "file": "sampleInsertions.txt.gz",
      "class": [
        "data.frame"
      ],
      "fields": [
        "position"
      ],
      "rows": 60,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "binHist",
      "title": "Histogram Breakpoints",
      "topics": [
        "binHist"
      ]
    },
    {
      "page": "binInsert",
      "title": "Insert Locations",
      "topics": [
        "binInsert"
      ]
    },
    {
      "page": "binInsertHist",
      "title": "Insert Locations Quickly",
      "topics": [
        "binInsertHist"
      ]
    },
    {
      "page": "checkFormat",
      "title": "Checks the Format of Annotation and Insertions",
      "topics": [
        "checkFormat"
      ]
    },
    {
      "page": "delta0",
      "title": "Number of New Knockouts",
      "topics": [
        "delta0"
      ]
    },
    {
      "page": "eMult",
      "title": "Expected Value of the Occupancy Distribution",
      "topics": [
        "eMult"
      ]
    },
    {
      "page": "etDelta",
      "title": "Number of New ORF Knockouts",
      "topics": [
        "etDelta"
      ]
    },
    {
      "page": "fCumul",
      "title": "Parametric Function for the Cumulative Occupancy Distribution",
      "topics": [
        "fCumul"
      ]
    },
    {
      "page": "fFit",
      "title": "Parametric Fit for the Cumulative Occupancy Distribution",
      "topics": [
        "fFit"
      ]
    },
    {
      "page": "loadAnnotation",
      "title": "Loads Annotation File",
      "topics": [
        "loadAnnotation"
      ]
    },
    {
      "page": "loadInsertions",
      "title": "Load Genome Annotation File",
      "topics": [
        "loadInsertions"
      ]
    },
    {
      "page": "occup2Negenes",
      "title": "Convert Occupancy Format to Negenes",
      "topics": [
        "occup2Negenes"
      ]
    },
    {
      "page": "sampleAnnotation",
      "title": "Annotation for a Hypothetical Prokayote",
      "topics": [
        "sampleAnnotation"
      ]
    },
    {
      "page": "sampleInsertions",
      "title": "Insertions for a Hypothetical Clonal Library",
      "topics": [
        "sampleInsertions"
      ]
    },
    {
      "page": "unbiasB0",
      "title": "Unbiased Estimator of the Number of Non-essential ORFs",
      "topics": [
        "unbiasB0"
      ]
    },
    {
      "page": "unbiasDelta0",
      "title": "Unbiased Number of New Knockouts",
      "topics": [
        "unbiasDelta0"
      ]
    },
    {
      "page": "varMult",
      "title": "Variance of the Occupancy Distribution",
      "topics": [
        "varMult"
      ]
    }
  ],
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "occugene.Rnw",
      "filename": "occugene.pdf",
      "title": "occugene",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-11-01 19:58:56",
      "modified": "2013-11-01 19:58:56",
      "commits": 1
    }
  ],
  "_score": 3.3010299956639813,
  "_indexed": true,
  "_nocasepkg": "occugene",
  "_universes": [
    "bioc"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-07-14T05:03:39.000Z",
      "distro": "resolute",
      "commit": "07cdca33f01c249a8819e08fb643141dc24b7c86",
      "fileid": "https://r2.ropensci.org/3b3978f72d82d1e3f7512356388fd2f0f702d737d4018bd5336e9a0069fbd54e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29307292903"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.73.0",
      "date": "2026-07-14T05:04:15.000Z",
      "distro": "resolute",
      "commit": "07cdca33f01c249a8819e08fb643141dc24b7c86",
      "fileid": "https://r2.ropensci.org/209b5d87ebfa06d055586bf5f91cd9c59b2e401fe6981c2fa25d7770db15e7df",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29307292903"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-07-14T05:02:02.000Z",
      "commit": "07cdca33f01c249a8819e08fb643141dc24b7c86",
      "fileid": "https://r2.ropensci.org/339bfb7dda0250f52b4a5d27afa9b6361a9ad4d3477db4ba591afec608e30364",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29307292903"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.73.0",
      "date": "2026-07-14T05:02:15.000Z",
      "commit": "07cdca33f01c249a8819e08fb643141dc24b7c86",
      "fileid": "https://r2.ropensci.org/d7e7a68f75312882c51edcba48ba6132f632ea62379251c88978b6d889979d9a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29307292903"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.73.0",
      "date": "2026-07-14T05:02:28.000Z",
      "commit": "07cdca33f01c249a8819e08fb643141dc24b7c86",
      "fileid": "https://r2.ropensci.org/af8c05ded8e8b559905c10923010aab4193a1a31db9a943dd9f2fccc6c9da7f7",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29307292903"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-07-14T05:01:55.000Z",
      "commit": "07cdca33f01c249a8819e08fb643141dc24b7c86",
      "fileid": "https://r2.ropensci.org/d485b4ab1e350c61afe4d46ab965f1a2fc5e51c96ffa7714b8cd2c317b317977",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29307292903"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-07-14T05:01:52.000Z",
      "commit": "07cdca33f01c249a8819e08fb643141dc24b7c86",
      "fileid": "https://r2.ropensci.org/839d4ed9acfdc5d07599f9123271ccd46bd5ab87558aa931d9624b9ddb985911",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29307292903"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.73.0",
      "date": "2026-07-14T05:01:51.000Z",
      "commit": "07cdca33f01c249a8819e08fb643141dc24b7c86",
      "fileid": "https://r2.ropensci.org/3658873e377bd3b9ca610e97fe8d946fd1a1ecc8cffc4810034decae78977028",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/29307292903"
    }
  ]
}